Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina

Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively

Permanent draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from root nodules of Comptonia peregrina

Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able to reinfect plants of the Betulaceae and Myricaceae families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively

Subdiffusive axial transport of granular materials in a long drum mixer

Granular mixtures rapidly segregate radially by size when tumbled in a partially filled horizontal drum. The smaller component moves toward the axis of rotation and forms a buried core, which then splits into axial bands. Models have generally assumed that the axial segregation is opposed by diffusion. Using narrow pulses of the smaller component as initial conditions, we have characterized axial transport in the core. We find that the axial advance of the segregated core is well described by a self-similar concentration profile whose width scales as $t^\alpha$, with $\alpha \sim 0.3 < 1/2$. Thus, the process is subdiffusive rather than diffusive as previously assumed. We find that $\alpha$ is nearly independent of the grain type and drum rotation rate within the smoothly streaming regime. We compare our results to two one-dimensional PDE models which contain self-similarity and subdiffusion; a linear fractional diffusion model and the nonlinear porous medium equation.Comment: 4 pages, 4 figures, 1 table. Submitted to Phys Rev Lett. For more info, see http://www.physics.utoronto.ca/nonlinear

Inferring the dynamics of ionic currents from recursive piecewise data assimilation of approximate neuron models

We construct neuron models from data by transferring information from an observed time series to the state variables and parameters of Hodgkin-Huxley models. When the learning period completes, the model will predict additional observations and its parameters uniquely characterise the complement of ion channels. However, the assimilation of biological data, as opposed to model data, is complicated by the lack of knowledge of the true neuron equations. Reliance on guessed conductance models is plagued with multi-valued parameter solutions. Here, we report on the distributions of parameters and currents predicted with intentionally erroneous models, over-specified models, and an approximate model fitting hippocampal neuron data. We introduce a recursive piecewise data assimilation (RPDA) algorithm that converges with near-perfect reliability when the model is known. When the model is unknown, we show model error introduces correlations between certain parameters. The ionic currents reconstructed from these parameters are excellent predictors of true currents and carry a higher degree of confidence, >95.5%, than underlying parameters, >53%. Unexpressed ionic currents are correctly filtered out even in the presence of mild model error. When the model is unknown, the covariance eigenvalues of parameter estimates are found to be a good gauge of model error. Our results suggest that biological information may be retrieved from data by focussing on current estimates rather than parameters

Autocatalytic plume pinch-off

A localized source of buoyancy flux in a non-reactive fluid medium creates a plume. The flux can be provided by either heat, a compositional difference between the fluid comprising the plume and its surroundings, or a combination of both. For autocatalytic plumes produced by the iodate-arsenous acid reaction, however, buoyancy is produced along the entire reacting interface between the plume and its surroundings. Buoyancy production at the moving interface drives fluid motion, which in turn generates flow that advects the reaction front. As a consequence of this interplay between fluid flow and chemical reaction, autocatalytic plumes exhibit a rich dynamics during their ascent through the reactant medium. One of the more interesting dynamical features is the production of an accelerating vortical plume head that in certain cases pinches-off and detaches from the upwelling conduit. After pinch-off, a new plume head forms in the conduit below, and this can lead to multiple generations of plume heads for a single plume initiation. We investigated the pinch-off process using both experimentation and simulation. Experiments were performed using various concentrations of glycerol, in which it was found that repeated pinch-off occurs exclusively in a specific concentration range. Autocatalytic plume simulations revealed that pinch-off is triggered by the appearance of accelerating flow in the plume conduit.Comment: 10 figures. Accepted for publication in Phys Rev E. See also http://www.physics.utoronto.ca/nonlinear/papers_chemwave.htm

tDCS-induced alterations in GABA concentration within primary motor cortex predict motor learning and motor memory: A 7T magnetic resonance spectroscopy study

Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique that alters cortical excitability in a polarity specific manner and has been shown to influence learning and memory. tDCS may have both on-line and after-effects on learning and memory, and the latter are thought to be based upon tDCS-induced alterations in neurochemistry and synaptic function. We used ultra-high-field (7 T) magnetic resonance spectroscopy (MRS), together with a robotic force adaptation and de-adaptation task, to investigate whether tDCS-induced alterations in GABA and Glutamate within motor cortex predict motor learning and memory. Note that adaptation to a robot-induced force field has long been considered to be a form of model-based learning that is closely associated with the computation and ‘supervised’ learning of internal ‘forward’ models within the cerebellum. Importantly, previous studies have shown that on-line tDCS to the cerebellum, but not to motor cortex, enhances model-based motor learning. Here we demonstrate that anodal tDCS delivered to the hand area of the left primary motor cortex induces a significant reduction in GABA concentration. This effect was specific to GABA, localised to the left motor cortex, and was polarity specific insofar as it was not observed following either cathodal or sham stimulation. Importantly, we show that the magnitude of tDCS-induced alterations in GABA concentration within motor cortex predicts individual differences in both motor learning and motor memory on the robotic force adaptation and de-adaptation task

Natural versus forced convection in laminar starting plumes

A starting plume or jet has a well-defined, evolving head that is driven through the surrounding quiescent fluid by a localized flux of either buoyancy or momentum, or both. We studied the scaling and morphology of starting plumes produced by a constant flux of buoyant fluid from a small, submerged outlet. The plumes were laminar and spanned a wide range of plume Richardson numbers Ri. Ri is the dimensionless ratio of the buoyancy forces to inertial effects, and is thus our measurements crossed over the transition between buoyancy-driven plumes and momentum-driven jets. We found that the ascent velocity of the plume, nondimensionalized by Ri, exhibits a power law relationship with Re, the Reynolds number of the injected fluid in the outlet pipe. We also found that as the threshold between buoyancy-driven and momentum-driven flow was crossed, two distinct types of plume head mophologies existed: confined heads, produced in the Ri > 1 regime, and dispersed heads, which are found in the Ri < 1 regime. Head dispersal is caused by a breakdown of overturning motion in the head, and a local Kelvin-Helmholtz instability on the exterior of the plume.Comment: 8 pages, 8 figures, accepted for publication in Physics of Fluids (final version with corrections

The Influence of Pain Distribution on Walking Velocity and Horizontal Ground Reaction Forces in Patients with Low Back Pain

Objective. The primary purpose of this paper was to evaluate the influence of pain distribution on gait characteristics in subjects with low back problems (LBP) during walking at preferred and fastest speeds. Design. Cross-sectional, observational study. Setting. Gait analysis laboratory in a health professions university. Participants. A convenience age- and gender-matched sample of 20 subjects with back pain only (BPO), 20 with referred leg pain due to back problems (LGP), and 20 pain-free individuals (CON). Methods and Measures. Subjects completed standardized self-reports on pain and disability and were videotaped as they walked at their preferred and fastest speeds along a walkway embedded with a force plate. Temporal and spatial gait characteristics were measured at the midsection of the walkway, and peak medial, lateral, anterior, and posterior components of horizontal ground reaction forces (hGRFs) were measured during the stance phase. Results. Patients with leg pain had higher levels of pain intensity and affect compared to those with back pain only (t = 4.91, P < .001 and t = 5.80, P < 0.001, resp.) and walking had an analgesic effect in the BPO group. Gait velocity was highest in the control group followed by the BPO and LGP group and differed between groups at both walking speeds (F2.57 = 13.62, P < .001 and F2.57 = 9.09, P < .001, for preferred and fastest speed condition, resp.). When normalized against gait velocity, the LGP group generated significantly less lateral force at the fastest walking speed (P = .005) and significantly less posterior force at both walking speeds (P ≤ .01) compared to the control group. Conclusions. Pain intensity and distribution differentially influence gait velocity and hGRFs during gait. Those with referred leg pain tend to utilize significantly altered gait strategies that are more apparent at faster walking speeds